Section 35. The commissioner may, after a hearing, order such alteration, repairs or change of grade of such ways as will in his judgment enable the petitioner to raise, erect and maintain such dam without overflowing or otherwise injuring such ways, and they may give written direction and authority to the petitioner to make at his own expense such alterations, changes of grade and repairs within a reasonable time. He shall record all such orders and shall cause certified copies thereof to be filed and recorded in the office of the clerk of each town in which such alterations, changes of grade or repairs are ordered.